Hi, this bug report has a time correlation to the upload of the new version of bowtie (1.2.1.1):
On Mon, Oct 30, 2017 at 09:08:15PM +0100, Lucas Nussbaum wrote: > Source: bioperl-run > Version: 1.7.2-1 > Severity: serious > ... > > Relevant part (hopefully): > > ok 9 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not > > present > > ok 10 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not > > present > > ok 11 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not > > present > > ok 12 # skip Required executable for Bio::Tools::Run::tRNAscanSE is not > > present > > ok > > > > Test Summary Report > > ------------------- > > t/Bowtie.t (Wstat: 512 Tests: 61 Failed: 2) > > Failed tests: 43, 45 > > Non-zero exit status: 2 > > Files=72, Tests=1690, 156 wallclock secs ( 0.24 usr 0.07 sys + 133.72 cusr > > 6.41 csys = 140.44 CPU) > > Result: FAIL > > Failed 1/72 test programs. 2/1690 subtests failed. > > dh_auto_test: perl Build test --verbose 1 returned exit code 255 > > debian/rules:32: recipe for target 'override_dh_auto_test' failed Earlier in the log: ... # Failed test 'bowtie success' # at t/Bowtie.t line 188. # '# reads processed: 2000 # # reads with at least one reported alignment: 2000 (100.00%) # # reads that failed to align: 0 (0.00%) # Reported 1000 paired-end alignments to 1 output stream(s) # ' # doesn't match '(?^:reads processed: 1000)' # Failed test 'bowtie success' # at t/Bowtie.t line 195. # '# reads processed: 2000 # # reads with at least one reported alignment: 2000 (100.00%) # # reads that failed to align: 0 (0.00%) # Reported 1000 paired-end alignments to 1 output stream(s) # ' # doesn't match '(?^:reads processed: 1000)' # Looks like you failed 2 tests of 61. t/Bowtie.t ..................... ... I suspect that some change between bowtie 1.2.0 and bowtie 1.2.1.1 is responsible for the issue in bioperl-run. I wonder whether tracking down this issue sounds interesting for somebody who knows (and uses) bowtie a bit. Kind regards Andreas. -- http://fam-tille.de